Variant rs10400305 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.748 in 152,362 control chromosomes in the GnomAD database, including 45,103 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.75 ( 45023 hom., cov: 32)

Exomes 𝑓: 0.87 ( 80 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.401

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.748

AC:

113721

AN:

152028

Hom.:

45010

Cov.:

show subpopulations

Gnomad AFR

AF:

0.462

Gnomad AMI

AF:

0.905

Gnomad AMR

AF:

0.853

Gnomad ASJ

AF:

0.875

Gnomad EAS

AF:

0.987

Gnomad SAS

AF:

0.885

Gnomad FIN

AF:

0.902

Gnomad MID

AF:

0.870

Gnomad NFE

AF:

0.836

Gnomad OTH

AF:

0.780

GnomAD4 exome

AF:

0.866

AC:

187

AN:

216

Hom.:

AF XY:

0.855

AC XY:

142

AN XY:

166

show subpopulations

Gnomad4 AFR exome

AF:

0.750

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

1.00

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.851

Gnomad4 OTH exome

AF:

1.00

GnomAD4 genome

AF:

0.748

AC:

113770

AN:

152146

Hom.:

45023

Cov.:

AF XY:

0.757

AC XY:

56336

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.462

Gnomad4 AMR

AF:

0.853

Gnomad4 ASJ

AF:

0.875

Gnomad4 EAS

AF:

0.987

Gnomad4 SAS

AF:

0.885

Gnomad4 FIN

AF:

0.902

Gnomad4 NFE

AF:

0.836

Gnomad4 OTH

AF:

0.782

Alfa

AF:

0.832

Hom.:

104018

Bravo

AF:

0.734

Asia WGS

AF:

0.903

AC:

3138

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.2

DANN

Benign

0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over